Chromosome 6
Chromosome 6 | |
---|---|
Type | Autosome |
Centromere position | Submetacentric[2] (59.8 Mbp[3]) |
Complete gene lists | |
CCDS | Gene list |
HGNC | Gene list |
UniProt | Gene list |
NCBI | Gene list |
External map viewers | |
Ensembl | Chromosome 6 |
Entrez | Chromosome 6 |
NCBI | Chromosome 6 |
UCSC | Chromosome 6 |
Full DNA sequences | |
RefSeq | NC_000006 (FASTA) |
GenBank | CM000668 (FASTA) |
Chromosome 6 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans more than 172 million base pairs (the building material of DNA) and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 100 genes related to the immune response, and plays a vital role in organ transplantation.
The evolution of human centromere 6
The
Genes
The
Number of genes
In 2003, the entirety of chromosome 6 was manually annotated for proteins, resulting in the identification of 1,557 genes, and 633 pseudogenes.[5]
The following are some of the newer gene count estimates. Because researchers use different approaches to
Estimated by | Protein-coding genes
|
Non-coding RNA genes | Pseudogenes | Source | Release date |
---|---|---|---|---|---|
CCDS | 996 | — | — | [1] | 2016-09-08 |
HGNC | 1,007 | 422 | 736 | [7] | 2017-05-12 |
Ensembl | 1,038 | 985 | 800 | [8] | 2017-03-29 |
UniProt | 1,111 | — | — | [9] | 2018-02-28 |
NCBI | 1,053 | 1,188 | 911 | [10][11][12] | 2017-05-19 |
Gene list
The following is a partial list of genes on human chromosome 6. For complete list, see the link in the infobox on the right.
p-arm
The following are some of the genes located on p-arm (short arm) of human chromosome 6:
- ADTRP: encoding protein Androgen-dependent TFPI-regulating protein
- APOM: encoding protein Apolipoprotein M (6p21.33)
- ARMC12: encoding protein Armadillo repeat containing 12
- ATXN1: encoding protein Ataxin 1 (6p16.3-p16.76)
- TSBP1: encoding protein TSBP1 (6p21.32)
- C6orf62: chromosome 6 open reading frame 62 (6p22.3)
- C6orf89: chromosome 6 open reading frame 89 (6p21.2)
- CDKAL1: CDK5 regulatory subunit associated protein 1 like 1 (6p22.3)
- COL11A2: collagen, type XI, alpha 2(6p21.3)
- CRIP3: encoding protein Cysteine rich protein 3
- CYP21A2: cytochrome P450, family 21, subfamily A, polypeptide 2 (6p21.33)
- DHX16: DEAH-box helicase 16 (6p21.33)
- DOM3Z: Decapping exoribonuclease (6p21.33)
- DSP: Desmoplakin gene linked to cardiomyopathy (6p24.3)
- ELOVL5: ELOVL fatty acid elongase 5 (6p12.1)
- FBXO9: F-box protein 9 (6p12.1)
- FOXP4-AS1: encoding protein FOXP4 antisense RNA 1
- FTH1P5: encoding protein Ferritin, heavy polypeptide 1 pseudogene 5
- G6B: Protein G6b (6p21.33)
- GCNT2: N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (6p24.3)
- GGNBP1: encoding protein Gametogenetin binding protein 1 (pseudogene)
- GMDS: GDP-mannose 4,6-dehydratase (6p25.3)
- GTPBP2: encoding protein Gtp binding protein 2
- HCG4P11: HLA complex group 4 pseudogene 11
- HFE: hemochromatosis (6p22.2)
- HIST1H2AH: histone cluster 1 H2A family member h (6p22.1)
- HLA-A, HLA-B, HLA-C: major histocompatibility complex (MHC), class I, A, B, and C loci. (6p21.3)
- heterodimer MHC class II, DQ: Celiac1, IDDM (6p21.3)
- HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5 forms HLA-DR, heterodimer MHC class II, DR (6p21.3) Mold / Biotoxin Susceptibility
- , MHC class II, DP (6p21.3)
- HLA-Cw*06:02: gene variation related to psoriasis (6p21.3)
- KAAG1: encoding protein Kidney associated antigen 1
- LOC100533655: encoding protein Aryl hydrocarbon receptor pseudogene
- LST1: leukocyte specific transcript 1 (6p21.33)
- LY6G6E encoding protein Lymphocyte antigen 6 complex, locus G6E (pseudogene) (6p21.33)
- MIR4640: microRNA 4640 (6p21.33)
- MLIP: muscular LMNA interaction protein (6p12.1)
- MRPS18B: mitochondrial ribosomal protein S18B (6p21.33)
- MUT: methylmalonyl Coenzyme A mutase (6p12.3)
- NHLRC1: NHL repeat containing E3 ubiquitin protein ligase 1 (6p22.3)
- NOL7: nucleolar protein 7 (6p23)
- NQO2: N-ribosyldihydronicotinamide:quinone reductase 2 (6p25.2)
- NRSN1: neurensin 1 (6p22.3)
- NUDT3: nudix hydrolase 3 (6p21.31)
- PFDN6: prefoldin subunit 6 (6p21.32)
- PHACTR1: phosphatase and actin regulator 1 (6p24.1)
- PKHD1: polycystic kidney and hepatic disease 1 (autosomal recessive) (6p21.2-p12)
- PRICKLE4: prickle planar cell polarity protein 4 (6p21.1)
- PRSS16: protease, serine 16 (6p22.1)
- PSMB8-AS1: PSMB8 antisense RNA 1 (head to head) (6p21.32)
- RAB44: encoding protein Rab44, member ras oncogene family
- RIPOR2: RHO family interacting cell polarization regulator 2 (6p22.3)
- RPL10A: encoding protein 60S ribosomal protein L10a (6p21.31)
- SKIV2L: Ski2 like RNA helicase (6p21.33)
- SSR1: signal sequence receptor subunit 1 (6p24.3)
- TCF19: transcription factor 19 (6p21.33)
- TCP11: t-complex 11 (6p21.31)
- TJAP1: tight junction associated protein 1 (6p21.1)
- TP53COR1 encoding protein Tumor protein p53 pathway corepressor 1 (non-protein coding)
- TMEM151B: encoding protein Transmembrane protein 151B
- TNXB: tenascin XB (6p21.3)
- TRAM2: translocation associated membrane protein 2 (6p12.2)
- TRIM38: encoding protein Tripartite motif containing 38
- TTBK1: encoding protein Tau tubulin kinase 1
- UBR2: ubiquitin protein ligase E3 component n-recognin 2 (6p21.2)
- UNC5CL: encoding protein Unc-5 homolog C (C. elegans)-like
- USP8P1: encoding protein Ubiquitin specific peptidase 8 pseudogene 1
- VEGF: vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)
- VPS52: GARP complex subunit
- VWA7: encoding protein Von willebrand factor a domain containing 7
- ZKSCAN4: encoding protein zinc finger with KRAB and SCAN domains 4
- ZNF76: zinc finger protein 76 (6p21.31)
- ZNF193: zinc finger protein 193 (6p22.1)
- ZNRD1: zinc ribbon domain containing 1 (6p22.1)
q-arm
The following are some of the genes located on q-arm (long arm) of human chromosome 6:
- AIM1: encoding protein Absent in melanoma 1 protein (6q21)
- AIG1: encoding protein Androgen-induced protein 1 (6q24.2)
- AKIRIN2: akirin 2 (6q15)
- ARG1: arginase 1 (6q23.2)
- BCKDHB: branched-chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) (6q14.1)
- BMIQ3: body mass index QTL 3
- TMEM242 encoding transmembrane protein TMEM242
- C6orf203: encoding protein Chromosome 6 open reading frame 203
- C6orf58: chromosome 6 open reading frame 58 (6q22.33)
- CFAP206: encoding protein Cilia And Flagella Associated Protein 206
- CMD1F: cardiomyopathy, dilated 1F
- CMD1K: cardiomyopathy, dilated 1K
- CNR1: cannabinoid 1 receptor (6q14-q15)[13]
- DACT2: encoding protein Dishevelled binding antagonist of beta catenin 2
- DFNB38: deafness, autosomal recessive 38
- DYX4: dyslexia susceptibility 4
- ECT2L: encoding protein Epithelial cell transforming sequence 2 oncogene-like
- ESR1: Estrogen receptor 1 (6q25)
- EYA4: eyes absent homolog 4 (Drosophila)(6q23.2)
- FBXL4: F-box and leucine rich repeat protein 4 (6q16.1-q16.2)
- FEB5: febrile convulsions 5
- HACE1: HECT domain and Ankyrin repeat containing, E3 ubiquitin protein ligase 1 (6q21)
- HEBP2: heme binding protein 2 (6q24.1)
- IDDM8: insulin dependent diabetes mellitus 8
- IDDM15: insulin dependent diabetes mellitus 15
- IFNGR: interferon-γ receptor gene (6q23-q24)
- IGF2R: insulin-like growth factor 2 receptor (6q25.3)
- IMPG1: interphotoreceptor matrix proteoglylcan 1 (6q14.1)
- KIAA0408
- LGSN: encoding protein lengsin
- LIN28B: lin-28 homolog B (6q16.3-q21)
- MAN1A1: mannosidase alpha class 1A member 1 (6q22.31)
- MB21D1: encoding protein Mab-21 domain containing 1
- MCDR1: macular dystrophy, retinal, 1
- MDN1: midasin AAA ATPase 1 (6q15)
- MOXD1: monooxygenase DBH like 1 (6q23.2)
- MTO1: mitochondrial tRNA translation optimization 1 (6q13)
- MRT18: mental retardation, non-syndromic, autosomal recessive
- MRT28: mental retardation, non-syndromic, autosomal recessive
- MTRF1L: mitochondrial translational release factor 1 like (6q25.2)
- MYO6: myosin VI (6q14.1)
- NHEG1: encoding protein Neuroblastoma highly expressed 1
- OA3: ocular albinism 3
- OPRM1: μ-opioid receptors (6q24-q25)
- OTSC7: otosclerosis 7
- PLG: plasminogen (6q26)
- PBCRA1
- PARK2: Parkinson disease (autosomal recessive, juvenile) 2, parkin (6q26)
- PCMT1: protein-L-isoaspartate (D-aspartate) O-methyltransferase (6q25.1)
- PERP: p53 apoptosis effector related to PMP-22 (6q23.3)
- PKIB: cAMP-dependent protein kinase inhibitor beta (6p22.31)
- PLAGL1: (6q24.2)
- QRSL1: encoding protein Glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1
- RCD1: retinal cone dystrophy 1
- RFPL4B: Ret finger protein like 4B
- RP63: retinitis pigmentosa 63
- SASH1: SAM and SH3 domain containing 1 (6q24.3-q25.1)
- SCZD5: schizophrenia disorder 5
- SEN6: senescence (cellular)-related 6
- SENP6: SUMO1/sentrin specific peptidase 6 (6q14.1)
- SERAC1: serine active site containing 1 (6q25.3)
- SERINC1: serine incorporator 1 (6q22.31)
- SF3B5: splicing factor 3b subunit 5 (6q24.2)
- SMAP1: small ArfGAP 1 (6q13)
- SOBP: sine oculis binding protein homolog (6q21)
- SPG25: spastic paraplegia 25
- ST8: suppression of tumorigenicity 8
- SYNJ2: synaptojanin 2 (6q25.3)
- brachyury transcription factor (more commonly known as the T gene) linked to Hepatocellular carcinoma and Chordoma (6q27)[14]
- TAAR1: trace amine associated receptor 1 (6q23.1)
- TAAR2: trace amine associated receptor 2 (6q24)
- TMEM200A: encoding protein Transmembrane protein 200A
- TSPYL1: TSPY like 1 (6q22.1)
- UNC93A: encoding protein Unc-93 homolog A (C. elegans)
- VNN1: vanin 1 (6q23.2)
- VNN2: vanin 2 (6q23.2)
- VTA1: Vesicle trafficking 1 (6q24.1-2)
- ZC2HC1: encoding protein Zinc finger C2HC-type containing 1B
- ZDHHC14: encoding protein Zinc finger, DHHC-type containing 14
Diseases and disorders
The following diseases are some of those related to genes on chromosome 6:
- ankylosing spondylitis, HLA-B
- collagenopathy, types II and XI
- Coeliac disease HLA-DQA1 & DQB1
- Ehlers-Danlos syndrome, classical, hypermobility, and Tenascin-X types
- Hashimoto's thyroiditis
- hemochromatosis
- Hemochromatosis type 1
- 21-hydroxylase deficiency
- maple syrup urine disease
- methylmalonic acidemia
- Autosomal nonsyndromic deafness
- North Carolina macular dystrophy
- otospondylomegaepiphyseal dysplasia
- Parkinson disease
- polycystic kidney disease
- porphyria
- porphyria cutanea tarda
- Rheumatoid arthritis, HLA-DR
- CIRS (Chronic Inflammatory Response Syndrome ), Sick Building Syndrome, Mold Toxin Susceptibility / Poisoning, HLA-DR/DQ
- Spinocerebellar ataxia type 1, ATXN1
- Stickler syndrome, COL11A2
- Systemic lupus erythematosus
- Diabetes mellitus type 1, HLA-DR, DQA1 & DQB1
- X-linked sideroblastic anemia
- Epilepsy
- Guillain Barre Syndrome
- Chordoma
- Hepatocellular carcinoma
- Schizophrenia
Cytogenetic band
Chr. | Arm[20] | Band[21] | ISCN start[22] |
ISCN stop[22] |
Basepair start |
Basepair stop |
Stain[23] | Density |
---|---|---|---|---|---|---|---|---|
6 | p | 25.3 | 0 | 118 | 1 | 2,300,000 | gneg | |
6 | p | 25.2 | 118 | 207 | 2,300,001 | 4,200,000 | gpos | 25 |
6 | p | 25.1 | 207 | 355 | 4,200,001 | 7,100,000 | gneg | |
6 | p | 24.3 | 355 | 548 | 7,100,001 | 10,600,000 | gpos | 50 |
6 | p | 24.2 | 548 | 592 | 10,600,001 | 11,600,000 | gneg | |
6 | p | 24.1 | 592 | 740 | 11,600,001 | 13,400,000 | gpos | 25 |
6 | p | 23 | 740 | 844 | 13,400,001 | 15,200,000 | gneg | |
6 | p | 22.3 | 844 | 1185 | 15,200,001 | 25,200,000 | gpos | 75 |
6 | p | 22.2 | 1185 | 1348 | 25,200,001 | 27,100,000 | gneg | |
6 | p | 22.1 | 1348 | 1585 | 27,100,001 | 30,500,000 | gpos | 50 |
6 | p | 21.33 | 1585 | 1718 | 30,500,001 | 32,100,000 | gneg | |
6 | p | 21.32 | 1718 | 1836 | 32,100,001 | 33,500,000 | gpos | 25 |
6 | p | 21.31 | 1836 | 2162 | 33,500,001 | 36,600,000 | gneg | |
6 | p | 21.2 | 2162 | 2310 | 36,600,001 | 40,500,000 | gpos | 25 |
6 | p | 21.1 | 2310 | 2755 | 40,500,001 | 46,200,000 | gneg | |
6 | p | 12.3 | 2755 | 3080 | 46,200,001 | 51,800,000 | gpos | 100 |
6 | p | 12.2 | 3080 | 3140 | 51,800,001 | 53,000,000 | gneg | |
6 | p | 12.1 | 3140 | 3377 | 5,300,0001 | 57,200,000 | gpos | 100 |
6 | p | 11.2 | 3377 | 3421 | 57,200,001 | 58,500,000 | gneg | |
6 | p | 11.1 | 3421 | 3554 | 58,500,001 | 59,800,000 | acen | |
6 | q | 11.1 | 3554 | 3658 | 59,800,001 | 62,600,000 | acen | |
6 | q | 11.2 | 3658 | 3732 | 62,600,001 | 62,700,000 | gneg | |
6 | q | 12 | 3732 | 4147 | 62,700,001 | 69,200,000 | gpos | 100 |
6 | q | 13 | 4147 | 4324 | 69,200,001 | 75,200,000 | gneg | |
6 | q | 14.1 | 4324 | 4621 | 75,200,001 | 83,200,000 | gpos | 50 |
6 | q | 14.2 | 4621 | 4709 | 83,200,001 | 84,200,000 | gneg | |
6 | q | 14.3 | 4709 | 4917 | 84,200,001 | 87,300,000 | gpos | 50 |
6 | q | 15 | 4917 | 5228 | 87,300,001 | 92,500,000 | gneg | |
6 | q | 16.1 | 5228 | 5613 | 92,500,001 | 98,900,000 | gpos | 100 |
6 | q | 16.2 | 5613 | 5687 | 98,900,001 | 100,000,000 | gneg | |
6 | q | 16.3 | 5687 | 5983 | 10,000,0001 | 105,000,000 | gpos | 100 |
6 | q | 21 | 5983 | 6531 | 10,500,0001 | 114,200,000 | gneg | |
6 | q | 22.1 | 6531 | 6753 | 114,200,001 | 117,900,000 | gpos | 75 |
6 | q | 22.2 | 6753 | 6872 | 117,900,001 | 118,100,000 | gneg | |
6 | q | 22.31 | 6872 | 7168 | 118,100,001 | 125,800,000 | gpos | 100 |
6 | q | 22.32 | 7168 | 7345 | 125,800,001 | 126,800,000 | gneg | |
6 | q | 22.33 | 7345 | 7642 | 126,800,001 | 130,000,000 | gpos | 75 |
6 | q | 23.1 | 7642 | 7923 | 13,000,0001 | 130,900,000 | gneg | |
6 | q | 23.2 | 7923 | 8145 | 130,900,001 | 134,700,000 | gpos | 50 |
6 | q | 23.3 | 8145 | 8352 | 134,700,001 | 138,300,000 | gneg | |
6 | q | 24.1 | 8352 | 8560 | 138,300,001 | 142,200,000 | gpos | 75 |
6 | q | 24.2 | 8560 | 8708 | 142,200,001 | 145,100,000 | gneg | |
6 | q | 24.3 | 8708 | 8886 | 145,100,001 | 148,500,000 | gpos | 75 |
6 | q | 25.1 | 8886 | 9078 | 148,500,001 | 152,100,000 | gneg | |
6 | q | 25.2 | 9078 | 9241 | 152,100,001 | 155,200,000 | gpos | 50 |
6 | q | 25.3 | 9241 | 9596 | 155,200,001 | 160,600,000 | gneg | |
6 | q | 26 | 9596 | 9774 | 160,600,001 | 164,100,000 | gpos | 50 |
6 | q | 27 | 9774 | 10100 | 164,100,001 | 170,805,979 | gneg |
References
- ^ a b "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". NCBI. CCDS Release 20 for Homo sapiens. 2016-09-08. Retrieved 2017-05-28.
- ISBN 978-1-136-84407-2.
- ^ a b Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- PMID 35357911.
- PMID 14574404.
- PMID 20441615.
- ^ "Statistics & Downloads for chromosome 6". HUGO Gene Nomenclature Committee. 2017-05-12. Archived from the original on 2017-08-18. Retrieved 2017-05-19.
- ^ "Chromosome 6: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
- ^ "Human chromosome 6: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
- ^ "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- ^ "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ( ("genetype miscrna"[Properties] OR "genetype ncrna"[Properties] OR "genetype rrna"[Properties] OR "genetype trna"[Properties] OR "genetype scrna"[Properties] OR "genetype snrna"[Properties] OR "genetype snorna"[Properties]) NOT "genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- ^ "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- S2CID 4356509.
- ^ "T brachyury transcription factor". T - T brachyury transcription factor - Genetics Home Reference.
- ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
- ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
- ISBN 978-3-318-02253-7.
- S2CID 16666470.
- ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- ^ "p": Short arm; "q": Long arm.
- ^ For cytogenetic banding nomenclature, see article locus.
- ^ a b These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for Human Cytogenetic Nomenclature (2013). Arbitrary unit.
- ^ gpos: Region which is positively stained by G banding, generally AT-rich and gene poor; gneg: Region which is negatively stained by G banding, generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk.
- Notes
- Some text in this article was taken from http://ghr.nlm.nih.gov/chromosome=6 Archived 2007-08-12 at the Wayback Machine (public domain)
Further reading
- Gilbert F (2002). "Chromosome 6". Genet Test. 6 (4): 341–58. PMID 12537662.
External links
- National Institutes of Health. "Chromosome 6". Genetics Home Reference. Archived from the original on 2007-08-12. Retrieved 2017-05-06.
- "Chromosome 6". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
- "Chromosome 6 Research Project". Parent-driven research for genotype-phenotype studies on chromosome 6 disorders. Retrieved 2017-06-17